Image-based overlay metrology may typically include determining relative offsets between two or more layers on a sample based on relative imaged positions of features of an overlay target in the different layers of interest. Accordingly, the accuracy of the overlay measurement may be sensitive to alignment errors of the overlay target in the metrology tool. Typical overlay metrology systems may align a sample once per wafer batch or measurement recipe. However, overlay measurements may be performed at various overlay targets distributed across a sample and the optimal alignment of each overlay target may not be the same due to sample variations, differences in target design, or the like. Accordingly, a single alignment of a sample may result in decreased overlay measurement precision due to localized variations of overlay targets. Therefore, it may be desirable to have systems and methods to efficiently align an overlay metrology system to any selected overlay target on a sample.